Kinetics of mineralization of phenols in lake water

Moving persistence assessments into the 21st century: A role for weight-of-evidence and overall persistence

Assessing the persistence of chemicals in the environment is a key element in existing regulatory frameworks to protect human health and ecosystems. Persistence in the environment depends on many fate processes, including abiotic and biotic transformations and physical partitioning, which depend on substances' physicochemical properties and environmental conditions. A main challenge in persistence assessment is that existing frameworks rely on simplistic and reductionist evaluation schemes that may lead substances to be falsely assessed as persistent or the other way around-to be falsely assessed as nonpersistent. Those evaluation schemes typically assess persistence against degradation half-lives determined in single-compartment simulation tests or against degradation levels measured in stringent screening tests. Most of the available test methods, however, do not apply to all types of substances, especially substances that are poorly soluble, complex in composition, highly sorptive, or volatile. In addition, the currently applied half-life criteria are derived mainly from a few legacy persistent organic pollutants, which do not represent the large diversity of substances entering the environment. Persistence assessment would undoubtedly benefit from the development of more flexible and holistic evaluation schemes including new concepts and methods. A weight-of-evidence (WoE) approach incorporating multiple influencing factors is needed to account for chemical fate and transformation in the whole environment so as to assess overall persistence. The present paper's aim is to begin to develop an integrated assessment framework that combines multimedia approaches to organize and interpret data using a clear WoE approach to allow for a more consistent, transparent, and thorough assessment of persistence. Integr Environ Assess Manag 2022;18:868-887. © 2021 ExxonMobil Biomedical Sciences, Inc. Integrated Environmental Assessment and Management published by Wiley Periodicals LLC on behalf of Society of Environmental Toxicology & Chemistry (SETAC).

Assessing Biodegradability of Chemical Compounds from Microbial Community Growth Using Flow Cytometry

Compound biodegradability tests with natural microbial communities form an important keystone in the ecological assessment of chemicals. However, biodegradability tests are frequently limited by a singular focus either on the chemical and potential transformation products or on the individual microbial species degrading the compound. Here, we investigated a methodology to simultaneously analyze community compositional changes and biomass growth on dosed test compound from flow cytometry (FCM) data coupled to machine-learned cell type recognition. We quantified the growth of freshwater microbial communities on a range of carbon dosages of three readily biodegradable reference compounds, phenol, 1-octanol, and benzoate, in comparison to three fragrances, methyl jasmonate, myrcene, and musk xylene (as a nonbiodegradable control). Compound mass balances with between 0.1 to 10 mg C · liter-1 phenol or 1-octanol, inferred from cell numbers, parent compound analysis, and CO2 evolution, as well as use of 14C-labeled compounds, showed between 6 and 25% mg C · mg C-1 substrate incorporation into biomass within 2 to 4 days and 25 to 45% released as CO2 In contrast, similar dosage of methyl jasmonate and myrcene supported slower (4 to 10 days) and less (2.6 to 6.6% mg C · mg C-1 with 4.9 to 22% CO2) community growth. Community compositions inferred from machine-learned cell type recognition and 16S rRNA amplicon sequencing showed substrate- and concentration-dependent changes, with visible enrichment of microbial subgroups already at 0.1 mg C · liter-1 phenol and 1-octanol. In general, community compositions were similar at the start and after the stationary phase of the microbial growth, except at the highest used substrate concentrations of 100 to 1,000 mg C · liter-1 Flow cytometry cell counting coupled to deconvolution of communities into subgroups is thus suitable to infer biodegradability of organic chemicals, permitting biomass balances and near-real-time assessment of relevant subgroup changes.IMPORTANCE The manifold effects of potentially toxic compounds on microbial communities are often difficult to discern. Some compounds may be transformed or completely degraded by few or multiple strains in the community, whereas others may present inhibitory effects. In this study, we benchmark a new method based on machine-learned microbial cell recognition to rapidly follow dynamic changes in aquatic communities. We further determine productive biodegradation upon dosing of a number of well-known readily biodegradable tester compounds at a variety of concentrations. Microbial community growth was quantified using flow cytometry, and the multiple cell parameters measured were used in parallel to deconvolute the community on the basis of similarity to previously standardized cell types. Biodegradation was further confirmed by chemical analysis, showing how distinct changes in specific populations correlate to degradation. The method holds great promise for near-real-time community composition changes and deduction of compound biodegradation in natural microbial communities.

In Silico Approach to Support that p-Nitrophenol Monooxygenase from Arthrobacter sp. Strain JS443 Catalyzes the Initial Two Sequential Monooxygenations

p-Nitrophenol (PNP), used primarily for manufacturing pesticides and dyes, has been recognized as a priority environmental pollutant. It is therefore important to reduce the input of this toxicant into the environment and to establish approaches for its removal from the contaminated sites. PNP monooxygenase, a novel enzyme from Gram-positive bacteria like Arthrobacter sp. and Bacillus sp., that comprises two components, a flavoprotein reductase and an oxygenase, catalyzes the initial two sequential monooxygenations to convert PNP to trihydroxybenzene. Accurate and reliable prediction of this enzyme-substrate interactions and binding affinity are of vital importance in understanding these catalytic mechanisms of the two sequential reactions. As crystal structure of the enzyme has not yet been published, we built a homology model for PNP monooxygenase using crystallized chlorophenol 4-monooxygenase from Burkholderia cepacia AC1100 (3HWC) as the template. The model was assessed for its reliability using PROCHECK, ERRAT and ProSA. Molecular docking of the physiological substrates, PNP and 4-nitrocatechol (4-NC), was carried out using Glide v5.7 implemented in Maestro v9.2, and the binding energies were calculated to substantiate the prediction. Docking complexes formed by molecular level interactions of PNP monooxygenase-PNP/4-NC without or with the cofactors, FAD and NADH, showed good correlation with the established experimental evidence that the two-component PNP monooxygenase catalyzes both the hydroxylation of PNP and the oxidative release of nitrite from 4-NC in B. sphaericus JS905. Furthermore, molecular dynamics simulations performed for docking complexes using Desmond v3.0 showed stable nature of the interactions as well.

In silico approach to support that p-nitrophenol monooxygenase from Arthrobacter sp. strain JS443 catalyzes the initial two sequential monooxygenations

p-Nitrophenol (PNP), used primarily for manufacturing pesticides and dyes, has been recognized as a priority environmental pollutant. It is therefore important to reduce the input of this toxicant into the environment and to establish approaches for its removal from the contaminated sites. PNP monooxygenase, a novel enzyme from Gram-positive bacteria like Arthrobacter sp. and Bacillus sp., that comprises two components, a flavoprotein reductase and an oxygenase, catalyzes the initial two sequential monooxygenations to convert PNP to trihydroxybenzene. Accurate and reliable prediction of this enzyme-substrate interactions and binding affinity are of vital importance in understanding these catalytic mechanisms of the two sequential reactions. As crystal structure of the enzyme has not yet been published, we built a homology model for PNP monooxygenase using crystallized chlorophenol 4-monooxygenase from Burkholderia cepacia AC1100 (3HWC) as the template. The model was assessed for its reliability using PROCHECK, ERRAT, WHATCHECK and ProSA. Molecular docking of the physiological substrates, PNP and 4-nitrocatechol (4-NC), was carried out using Glide v5.7 implemented in Maestro v9.2, and the binding energies were calculated to substantiate the prediction. Docking complexes formed by molecular level interactions of PNP monooxygenase-PNP/4-NC without or with the cofactors, FAD and NADH, showed good correlation with the established experimental evidence that the two-component PNP monooxygenase catalyzes both the hydroxylation of PNP and the oxidative release of nitrite from 4-NC in B. sphaericus JS905. Furthermore, molecular dynamics simulations performed for docking complexes using Desmond v3.0 showed stable nature of the interactions as well.

A model framework to describe growth-linked biodegradation of trace-level pollutants in the presence of coincidental carbon substrates and microbes

Pollutants such as pesticides and their degradation products occur ubiquitously in natural aquatic environments at trace concentrations (μg L(-1) and lower). Microbial biodegradation processes have long been known to contribute to the attenuation of pesticides in contaminated environments. However, challenges remain in developing engineered remediation strategies for pesticide-contaminated environments because the fundamental processes that regulate growth-linked biodegradation of pesticides in natural environments remain poorly understood. In this research, we developed a model framework to describe growth-linked biodegradation of pesticides at trace concentrations. We used experimental data reported in the literature or novel simulations to explore three fundamental kinetic processes in isolation. We then combine these kinetic processes into a unified model framework. The three kinetic processes described were: the growth-linked biodegradation of micropollutant at environmentally relevant concentrations; the effect of coincidental assimilable organic carbon substrates; and the effect of coincidental microbes that compete for assimilable organic carbon substrates. We used Monod kinetic models to describe substrate utilization and microbial growth rates for specific pesticide and degrader pairs. We then extended the model to include terms for utilization of assimilable organic carbon substrates by the specific degrader and coincidental microbes, growth on assimilable organic carbon substrates by the specific degrader and coincidental microbes, and endogenous metabolism. The proposed model framework enables interpretation and description of a range of experimental observations on micropollutant biodegradation. The model provides a useful tool to identify environmental conditions with respect to the occurrence of assimilable organic carbon and coincidental microbes that may result in enhanced or reduced micropollutant biodegradation.

Kinetics of mixed microbial assemblages enhance removal of highly dilute organic substrates

Our experiments with selected organic substrates reveal that the rate-limiting process governing microbial degradation rates changes with substrate concentration, S, in such a manner that substrate removal is enhanced at lower values of S. This enhancement is the result of the dominance of very efficient systems for substrate removal at low substrate concentrations. The variability of dominant kinetic parameters over a range of S causes the kinetics of complex assemblages to be profoundly dissimilar to those of systems possessing a single set of kinetic parameters; these findings necessitate taking a new approach to predicting substrate removal rates over wide ranges of S.

Monod kinetics rather than a first-order degradation model explains atrazine fate in soil mini-columns: implications for pesticide fate modelling

Pesticide transport models commonly assume first-order pesticide degradation kinetics for describing reactive transport in soil. This assumption was assessed in mini-column studies with associated batch degradation tests. Soil mini-columns were irrigated with atrazine in two intermittent steps of about 30 days separated by 161 days application of artificial rain water. Atrazine concentration in the effluent peaked to that of the influent concentration after initial break-through but sharply decreased while influx was sustained, suggesting a degradation lag phase. The same pattern was displayed in the second step but peak height and percentage of atrazine recovered in the effluent were lower. A Monod model with biomass decay was successfully calibrated to this data. The model was successfully evaluated against batch degradation data and mini-column experiments at lower flow rate. The study suggested that first-order degradation models may underestimate risk of pesticide leaching if the pesticide degradation potential needs amplification during degradation.

2,4-Dichlorophenoxyacetic acid (2,4-D) biodegradation in river sediments of Northeast-Scotland and its effect on the microbial communities (PLFA and DGGE)

A bench-scale study was conducted to investigate 2,4-D biodegradation rates at different concentrations (10, 100 and 1000 microg per gram of dry weight) in distinct sediments samples collected on the River Ythan, Northeast-Scotland. Mineralisation of 14C 2,4-D occurred mostly within 30 days for all tested concentrations with a degradation rate ranging from 5 to 750 microg d(-1). Biodegradation rates were affected by the biological and biochemical characteristics of the indigenous microbial community in the studied sediments rather than factors such as compound bioavailability and/or toxicity. PLFA-profiling provided evidences of the effect of 2,4-D amendments on the microbial communities and DGGE-profiling showed changes in the genetic potential of the microbial populations which might affect metabolic characteristics of the sediment. PLFAs biomarkers suggested that the pathway of alpha-ketoglutarate-dependent dioxygenase was the main route of 2,4-D biodegradation. This pathway is commonly found in microorganisms of the beta-subdivision of proteobacteria.

Mineralization of a sorbed polycyclic aromatic hydrocarbon in two soils using catalyzed hydrogen peroxide

Hydrogen peroxide (H2O2) catalyzed by soluble iron or naturally occurring soil minerals, (i.e., modified Fenton's reagent) was investigated as a basis for mineralizing sorbed and NAPL-phase benzo[a]pyrene (BaP), a hydrophobic and toxic polycyclic aromatic hydrocarbon, in two soils of different complexity. 14C-Benzo[a]pyrene was added to silica sand and a silt loam soil, and mineralization was investigated using three-level central composite rotatable experimental designs. The effects of H2O2 concentration, slurry volume, and iron(II) amendment were investigated in the silica sand systems. In a Palouse loess silt loam soil, the variables included H2O2 concentration, slurry volume, and pH, with H2O2 catalyzed by naturally occurring iron oxyhydroxides. Regression equations generated from the data were used to develop three-dimensional response surfaces describing BaP mineralization. Based on the recovery of 14C-CO2, 70% BaP mineralization was achieved in the sand within 24 h using 15 M H2O2 and an iron(II) concentration of 6.6 mM with a slurry volume of 0.3 x the field capacity of the sand. For the silt loam soil, 85% mineralization of BaP was observed using 15 M H2O2, no iron amendment, and a slurry volume of 20 x the soil field capacity. The balance of the radiolabeled carbon remained as unreacted BaP in the soil fraction. Gas-purge measurements over 5 d confirmed negligible desorption under nontreatment conditions. However, oxidation reactions were complete within 24 h and promoted up to 85% BaP mineralization, documenting that the natural rate of desorption/dissolution did not control the rate of oxidation and mineralization of the BaP. The results show that catalyzed H2O2 has the ability to rapidly mineralize sorbed/NAPL-phase BaP and that partitioning, which is often the rate-limiting factor in soil remediation, does not appear to limit the rate of vigorous Fenton-like treatment.

Growth kinetics of suspended microbial cells: from single-substrate-controlled growth to mixed-substrate kinetics

Growth kinetics, i.e., the relationship between specific growth rate and the concentration of a substrate, is one of the basic tools in microbiology. However, despite more than half a century of research, many fundamental questions about the validity and application of growth kinetics as observed in the laboratory to environmental growth conditions are still unanswered. For pure cultures growing with single substrates, enormous inconsistencies exist in the growth kinetic data reported. The low quality of experimental data has so far hampered the comparison and validation of the different growth models proposed, and only recently have data collected from nutrient-controlled chemostat cultures allowed us to compare different kinetic models on a statistical basis. The problems are mainly due to (i) the analytical difficulty in measuring substrates at growth-controlling concentrations and (ii) the fact that during a kinetic experiment, particularly in batch systems, microorganisms alter their kinetic properties because of adaptation to the changing environment. For example, for Escherichia coli growing with glucose, a physiological long-term adaptation results in a change in KS for glucose from some 5 mg liter-1 to ca. 30 microg liter-1. The data suggest that a dilemma exists, namely, that either "intrinsic" KS (under substrate-controlled conditions in chemostat culture) or micromax (under substrate-excess conditions in batch culture) can be measured but both cannot be determined at the same time. The above-described conventional growth kinetics derived from single-substrate-controlled laboratory experiments have invariably been used for describing both growth and substrate utilization in ecosystems. However, in nature, microbial cells are exposed to a wide spectrum of potential substrates, many of which they utilize simultaneously (in particular carbon sources). The kinetic data available to date for growth of pure cultures in carbon-controlled continuous culture with defined mixtures of two or more carbon sources (including pollutants) clearly demonstrate that simultaneous utilization results in lowered residual steady-state concentrations of all substrates. This should result in a competitive advantage of a cell capable of mixed-substrate growth because it can grow much faster at low substrate concentrations than one would expect from single-substrate kinetics. Additionally, the relevance of the kinetic principles obtained from defined culture systems with single, mixed, or multicomponent substrates to the kinetics of pollutant degradation as it occurs in the presence of alternative carbon sources in complex environmental systems is discussed. The presented overview indicates that many of the environmentally relevant apects in growth kinetics are still waiting to be discovered, established, and exploited.

Stability of 1-nitropyrene and 1,6-dinitropyrene in environmental water samples and soil suspensions

This study examined the stability of mutagenic 1-nitropyrene (1-NP) and (1,6-dinitropyrene (1,6-diNP) in environmental water samples and various soil suspensions containing 0.1% peptone and in water samples containing no peptone. The water samples or the soil suspensions were mixed with NPs and incubated at 30 degrees C. The stability of NPs was expressed as mutagenic activity remaining in the test solutions. The mutagenicity decreased rapidly when 1-NP or 1,6-diNP was incubated in unautoclaved test solutions containing 0.1% peptone but not when incubated in autoclaved test solutions. The mutagenicity in the soil suspensions, especially in the sludge, decreased faster than in the water samples. This was due to the large number of colony-forming units (CFU) in the soil suspensions. In the water samples containing 0.1% peptone, the mutagenicity of NPs in the polluted Tamiya River water decreased faster than in the unpolluted Yoshino River water. The rate of decrease was dependent on the number of CFU in the water samples. A large number of CFU decreased the mutagenicity more rapidly than did a small number of CFU in samples. The disappearance of mutagenicity was dependent on the initial concentrations of NPs. The periods required for a 50% decrease in the mutagenicity of 1-NP at the low concentration (0.2 microgram/ml) was shorter than that at the high concentration (3 micrograms/ml). 1-Aminopyrene was detected in the 1-NP test solution after incubation when it was analyzed by high-pressure liquid chromatography. In the water samples containing no peptone, the mutagenicity of 1-NP (0.2 microgram/ml) decreased gradually during 30 days of incubation. After incubation for 1540 days, the remaining mutagenicity of 1-NP in the water samples was almost the same as that in autoclaved water samples. On the other hand, the mutagenicity of 1,6-diNP (10 ng/ml) decreased and the remaining mutagenicity, except in the Yoshino River water, was less than 20% after 30 days of incubation and was completely lost during the 1540-day incubation. However, the mutagenicity of 1,6-diNP in autoclaved water samples was very stable and almost all mutagenicity, except in sea water, remained after 1540 days of incubation at 30 degrees C. These results suggest that the microflora in the environment plays an important role in the primary degradation and decontamination of relatively low concentrations of NPs.

Microbiological and biotechnological aspects of metabolism of carbamates and organophosphates

Several carbamate and organophosphate compounds are used to control a wide variety of insect pests, weeds, and disease-transmitting vectors. These chemicals were introduced to replace the recalcitrant and hazardous chlorinated pesticides. Although newly introduced pesticides were considered to be biodegradable, some of them are highly toxic and their residues are found in certain environments. In addition, degradation of some of the carbamates generates metabolites that are also toxic. In general, hydrolysis of the carbamate and organophosphates yields less toxic metabolites compared with the metabolites produced from oxidation. Although microorganisms capable of degrading many of these pesticides have been isolated, knowledge about the biochemical pathways and respective genes involved in the degradation is sparse. Recently, a great deal of interest in the mechanisms of biodegradation of carbamate and organophosphate compounds has been shown because (1) an efficient mineralization of the pesticides used for insect control could eliminate the problems of environmental pollution, (2) a balance between degradation and efficacy of pesticides could result in safer application and effective insect control, and (3) knowledge about the mechanisms of biodegradation could help to deal with situations leading to the generation of toxic metabolites and bioremediation of polluted environments. In addition, advances in genetic engineering and biotechnology offer great potential to exploit the degradative properties of microorganisms in order to develop bioremediation strategies and novel applications such as development of economic plants tolerant to herbicides. In this review, recent advances in the biochemical and genetic aspects of microbial degradation of carbamate and organophosphates are discussed and areas in need of further investigation identified.

Biodegradation of p-nitrophenol in an aqueous waste stream by immobilized bacteria

Microbiological analyses of activated sludge reactors after repeated exposure to 100 mg of p-nitrophenol (PNP) per liter resulted in the isolation of three Pseudomonas species able to utilize PNP as a sole source of carbon and energy. Cell suspensions of the three Pseudomonas sp., designated PNP1, PNP2, and PNP3, mineralized 70, 60, and 45% of a 70-mg/liter dose of PNP in 24, 48, and 96 h, respectively. Mass-balance analyses of PNP residues for all three cultures showed that undegraded PNP was less than 1% (less than 50 micrograms); volatile metabolites, less than 1%; cell residues, 8.4 to 14.9%; and water-soluble metabolites, 1.2 to 6.7%. A mixed culture of all three PNP-degrading Pseudomonas sp. was immobilized by adsorption onto diatomaceous earth biocarrier in a 1.75-liter Plexiglas column. The column was aerated and exposed to a synthetic waste stream containing 629 to 2,513 mg of PNP per liter at flow rates of 2 to 15 ml/min. Chemical loading studies showed that the threshold concentration for acute toxicity of PNP to the immobilized bacteria was 2,100 to 2,500 mg/liter. Further studies at PNP concentrations of 1,200 to 1,800 mg/liter showed that greater than 99 and 91 to 99% removal of PNP was achieved by immobilized bacteria at flow rates of 10 and 12 ml/min, respectively. These values represent hydraulic retention times of 48 to 58 min and PNP removal rates of 0.99 to 1.1 mg/h per g of biocarrier at 25 degrees C under optimal conditions. This study shows the successful use of immobilized bacteria technology to remove high concentrations of PNP from aqueous waste streams.

Effects and fate of phenol in simulated landfill sites

Phenol was administered to landfill waste in concentrations from 150 to 1,000 ppm via the feed-liquor of lysimeter systems over an 18-week incubation period. Biotic contributions to phenol removal in the landfill waste were of greater significance than abiotic removal. The addition of phenol did not cause the isolation of thermophilic phenol degraders. Plates inoculated from the test lysimeter receiving phenol were eventually predominated by mesophilic phenol-degradingMicrococcus, Nocardia, andArthrobacter spp.; plates inoculated from the control lysimeter, receiving water, were predominated by species incapable of utilizing phenol.

Explanations for the acclimation period preceding the mineralization of organic chemicals in aquatic environments

A study was conducted of possible reasons for acclimation of microbial communities to the mineralization of organic compounds in lake water and sewage. The acclimation period for the mineralization of 2 ng of p-nitrophenol (PNP) or 2,4-dichlorophenoxyacetic acid per ml of sewage was eliminated when the sewage was incubated for 9 or 16 days, respectively, with no added substrate. The acclimation period for the mineralization of 2 ng but not 200 ng or 2 micrograms of PNP per ml was eliminated when the compound was added to lake water that had been first incubated in the laboratory. Mineralization of PNP by Flavobacterium sp. was detected within 7 h at concentrations of 20 ng/ml to 2 micrograms/ml but only after 25 h at 2 ng/ml. PNP-utilizing organisms began to multiply logarithmically after 1 day in lake water amended with 2 micrograms of PNP per ml, but substrate disappearance was only detected at 8 days, at which time the numbers were approaching 10(5) cells per ml. The addition of inorganic nutrients reduced the length of the acclimation period from 6 to 3 days in sewage and from 6 days to 1 day in lake water. The prior degradation of natural organic materials in the sewage and lake water had no effect on the acclimation period for the mineralization of PNP, and naturally occurring inhibitors that might delay the mineralization were not present. The length of the acclimation phase for the mineralization of 2 ng of PNP per ml was shortened when the protozoa in sewage were suppressed by eucaryotic inhibitors, but it was unaffected or increased if the inhibitors were added to lake water.(ABSTRACT TRUNCATED AT 250 WORDS)